Improvements And Extensions To The Blast Algorithms

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The program tblastn has been modified so that its substitution matrix may be modified by either compositional scaling or conditional compositional matrix adjustment. Because the query is a DNA sequence that is conceptually is translated in six frames, at least five of which are usually incorrect, matrix modification requires the definition of a sequence window from which to calculate sequence composition. We have constructed a way to define such a window that yields good empirical results. Our studies have shown that either type of substitution matrix modification yields statistics that are much more accurate than those of the baseline program, with only a minor attendant decrease in retrieval accuracy. Further work this year has focussed on extending PSI-BLAST so that it is able to use information on correlated sequence positions deduced from multiple alignments.